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Home / Equine Research Bank / Proc Natl Acad Sci U S A / Speciation with gene flow in equids despite extensive chromo...
Proceedings of the National Academy of Sciences of the United States of America2014; 111(52); 18655-18660; doi: 10.1073/pnas.1412627111

Speciation with gene flow in equids despite extensive chromosomal plasticity.

Abstract: Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.
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Publication Date: 2014-12-01 PubMed ID: 25453089PubMed Central: PMC4284605DOI: 10.1073/pnas.1412627111Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research study focuses on the genetic evolution of equine species – horses, asses, and zebras. Despite significant chromosomal changes, evidence of gene flow and speciation was found among all of these species, providing insights on how chromosomal structure influences gene flow and speciation.

Research Objective and Methodology

  • The research aims to understand the genetic evolution and speciation among equine species, including horses, asses, and zebras, despite their chromosomal differences. The genus Equus emerged around 4.0 to 4.5 million years ago (Mya), and the succession of events leading to the diversity of species today remains unclear.
  • For the analysis, the researchers sequenced six genomes from each extant species of asses and zebras. The genome of an extinct quagga zebra was also characterized using a museum specimen.

Key Findings

  • The researchers identified 48 genes that evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. This suggests that these genes might play a key role in the specific adaptations of the equine species.
  • The study presents a dynamic demographic history of equids, with synchronous expansions and collapses on different continents during the last 400,000 years, majorly influenced by climatic events.
  • The earliest speciation was found to have occurred in Northern America, with the ancestors of today’s asses and zebras dispersing into the Old World (Eurasia and Africa) 2.1 to 3.4 Mya.
  • Despite the difference in chromosomal count varying from 16 pairs to 31 pairs, evidence for gene flow amongst three contemporary equine species was found. This challenges the belief that accumulation of chromosomal rearrangements leads to complete reproductive isolation.

Implications of the Study

  • The findings promote equids as a primary model for understanding the relationship between chromosomal structure, gene flow, and speciation.
  • This study could impact future research on genetic evolution and offer a greater understanding of how species diversify over time.
  • It also provides a genomic basis for past demographic events impacting equine species, opening avenues for studying the impact of climatic and environmental changes on genetic diversification.

Cite This Article

APA
Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. (2014). Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc Natl Acad Sci U S A, 111(52), 18655-18660. https://doi.org/10.1073/pnas.1412627111

Publication

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
NlmUniqueID: 7505876
Country: United States
Language: English
Volume: 111
Issue: 52
Pages: 18655-18660

Researcher Affiliations

Jónsson, Hákon
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Schubert, Mikkel
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Seguin-Orlando, Andaine
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark; National High-Throughput DNA Sequencing Center, DK-1353 Copenhagen K, Denmark;
Ginolhac, Aurélien
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Petersen, Lillian
  • National High-Throughput DNA Sequencing Center, DK-1353 Copenhagen K, Denmark;
Fumagalli, Matteo
  • Department of Integrative Biology, University of California, Berkeley, CA 94720; UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom;
Albrechtsen, Anders
  • The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark;
Petersen, Bent
  • Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark;
Korneliussen, Thorfinn S
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Vilstrup, Julia T
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Lear, Teri
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Myka, Jennifer Leigh
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Lundquist, Judith
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Miller, Donald C
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853;
Alfarhan, Ahmed H
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Alquraishi, Saleh A
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Al-Rasheid, Khaled A S
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Stagegaard, Julia
  • Ree Park, Ebeltoft Safari, DK-8400 Ebeltoft, Denmark;
Strauss, Günter
  • Tierpark Berlin-Friedrichsfelde, 10319 Berlin, Germany; and.
Bertelsen, Mads Frost
  • Centre for Zoo and Wild Animal Health, Copenhagen Zoo, DK-2000 Frederiksberg, Denmark.
Sicheritz-Ponten, Thomas
  • Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark;
Antczak, Douglas F
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853;
Bailey, Ernest
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Nielsen, Rasmus
  • Department of Integrative Biology, University of California, Berkeley, CA 94720;
Willerslev, Eske
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark; Lorlando@snm.ku.dk.

MeSH Terms

  • Africa
  • Animals
  • Chromosomes, Mammalian / genetics
  • Equidae / genetics
  • Evolution, Molecular
  • Extinction, Biological
  • Gene Flow
  • North America

Conflict of Interest Statement

The authors declare no conflict of interest.

References

This article includes 49 references
  1. Macfadden BJ. Evolution. Fossil horses--evidence for evolution.. Science 2005 Mar 18;307(5716):1728-30.
    pubmed: 15774746doi: 10.1126/science.1105458google scholar: lookup
  2. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. Nature 2013 Jul 4;499(7456):74-8.
    pubmed: 23803765doi: 10.1038/nature12323google scholar: lookup
  3. Moehlman PD, Shah N, Feh C. Equus hemionus. .
  4. Moehlman PD, Yohannes H, Teclai R, Kebede F. Equus africanus. .
  5. Moehlman PD, Rubenstein DI, Kebede F. Equus grevyi. .
  6. Weinstock J, Willerslev E, Sher A, Tong W, Ho SY, Rubenstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Xulong L, Cooper A. Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective.. PLoS Biol 2005 Aug;3(8):e241.
    pmc: PMC1159165pubmed: 15974804doi: 10.1371/journal.pbio.0030241google scholar: lookup
  7. Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R, Shockey BJ, Wrinn PJ, Vasil'ev SK, Ovodov ND, Cherry MI, Hopwood B, Male D, Austin JJ, Hänni C, Cooper A. Revising the recent evolutionary history of equids using ancient DNA.. Proc Natl Acad Sci U S A 2009 Dec 22;106(51):21754-9.
    pmc: PMC2799835pubmed: 20007379doi: 10.1073/pnas.0903672106google scholar: lookup
  8. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
    pmc: PMC3785132pubmed: 19892987doi: 10.1126/science.1178158google scholar: lookup
  9. Andersson LS, Larhammar M, Memic F, Wootz H, Schwochow D, Rubin CJ, Patra K, Arnason T, Wellbring L, Hjälm G, Imsland F, Petersen JL, McCue ME, Mickelson JR, Cothran G, Ahituv N, Roepstorff L, Mikko S, Vallstedt A, Lindgren G, Andersson L, Kullander K. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice.. Nature 2012 Aug 30;488(7413):642-6.
    pmc: PMC3523687pubmed: 22932389doi: 10.1038/nature11399google scholar: lookup
  10. Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. Mitochondrial phylogenomics of modern and ancient equids.. PLoS One 2013;8(2):e55950.
    pmc: PMC3577844pubmed: 23437078doi: 10.1371/journal.pone.0055950google scholar: lookup
  11. Steiner CC, Ryder OA. Molecular phylogeny and evolution of the Perissodactyla. Zool J Linn Soc 2011;163:1289–1303.
  12. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.. PLoS Genet 2012 Jan;8(1):e1002451.
    pmc: PMC3257288pubmed: 22253606doi: 10.1371/journal.pgen.1002451google scholar: lookup
  13. Lorenzen ED, Arctander P, Siegismund HR. High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites.. Mol Ecol 2008 Jun;17(12):2812-24.
    pubmed: 18466230doi: 10.1111/j.1365-294x.2008.03781.xgoogle scholar: lookup
  14. Kimura B, Marshall FB, Chen S, Rosenbom S, Moehlman PD, Tuross N, Sabin RC, Peters J, Barich B, Yohannes H, Kebede F, Teclai R, Beja-Pereira A, Mulligan CJ. Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication.. Proc Biol Sci 2011 Jan 7;278(1702):50-7.
    pmc: PMC2992715pubmed: 20667880doi: 10.1098/rspb.2010.0708google scholar: lookup
  15. Bowling AT, Zimmermann W, Ryder O, Penado C, Peto S, Chemnick L, Yasinetskaya N, Zharkikh T. Genetic variation in Przewalski's horses, with special focus on the last wild caught mare, 231 Orlitza III.. Cytogenet Genome Res 2003;102(1-4):226-34.
    pubmed: 14970708doi: 10.1159/000075754google scholar: lookup
  16. Leonard JA, Rohland N, Glaberman S, Fleischer RC, Caccone A, Hofreiter M. A rapid loss of stripes: the evolutionary history of the extinct quagga.. Biol Lett 2005 Sep 22;1(3):291-5.
    pmc: PMC1617154pubmed: 17148190doi: 10.1098/rsbl.2005.0323google scholar: lookup
  17. Musilova P, Kubickova S, Vahala J, Rubes J. Subchromosomal karyotype evolution in Equidae.. Chromosome Res 2013 Apr;21(2):175-87.
    pubmed: 23532666doi: 10.1007/s10577-013-9346-zgoogle scholar: lookup
  18. Faria R, Navarro A. Chromosomal speciation revisited: rearranging theory with pieces of evidence.. Trends Ecol Evol 2010 Nov;25(11):660-9.
    pubmed: 20817305doi: 10.1016/j.tree.2010.07.008google scholar: lookup
  19. Stevison LS, Hoehn KB, Noor MA. Effects of inversions on within- and between-species recombination and divergence.. Genome Biol Evol 2011;3:830-41.
    pmc: PMC3171675pubmed: 21828374doi: 10.1093/gbe/evr081google scholar: lookup
  20. Eisenmann V. Origins, dispersals, and migrations of Equus (Mammalia, Perissodactyla). Cour Forschungsinstitut Senckenb 1992;153:161–170.
  21. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. DNA sequences from the quagga, an extinct member of the horse family.. Nature 1984 Nov 15-21;312(5991):282-4.
    pubmed: 6504142doi: 10.1038/312282a0google scholar: lookup
  22. Murphy WJ, Stanyon R, O'Brien SJ. Evolution of mammalian genome organization inferred from comparative gene mapping.. Genome Biol 2001;2(6):REVIEWS0005.
    pmc: PMC138942pubmed: 11423011doi: 10.1186/gb-2001-2-6-reviews0005google scholar: lookup
  23. Tomiyasu A, Nakamura M, Ichiba M, Ueno S, Saiki S, Morimoto M, Kobal J, Kageyama Y, Inui T, Wakabayashi K, Yamada T, Kanemori Y, Jung HH, Tanaka H, Orimo S, Afawi Z, Blatt I, Aasly J, Ujike H, Babovic-Vuksanovic D, Josephs KA, Tohge R, Rodrigues GR, Dupré N, Yamada H, Yokochi F, Kotschet K, Takei T, Rudzińska M, Szczudlik A, Penco S, Fujiwara M, Tojo K, Sano A. Novel pathogenic mutations and copy number variations in the VPS13A gene in patients with chorea-acanthocytosis.. Am J Med Genet B Neuropsychiatr Genet 2011 Jul;156B(5):620-31.
    pubmed: 21598378doi: 10.1002/ajmg.b.31206google scholar: lookup
  24. Shimo H, Nakamura M, Tomiyasu A, Ichiba M, Ueno S, Sano A. Comprehensive analysis of the genes responsible for neuroacanthocytosis in mood disorder and schizophrenia.. Neurosci Res 2011 Mar;69(3):196-202.
    pubmed: 21145924doi: 10.1016/j.neures.2010.12.001google scholar: lookup
  25. Fiore R, Rahim B, Christoffels VM, Moorman AF, Püschel AW. Inactivation of the Sema5a gene results in embryonic lethality and defective remodeling of the cranial vascular system.. Mol Cell Biol 2005 Mar;25(6):2310-9.
    pmc: PMC1061610pubmed: 15743826doi: 10.1128/mcb.25.6.2310-2319.2005google scholar: lookup
  26. Zhu B, Chen C, Xue G, Moyzis RK, Dong Q, Chen C, Li J, He Q, Lei X, Wang Y, Lin C. The SEMA5A gene is associated with hippocampal volume, and their interaction is associated with performance on Raven's Progressive Matrices.. Neuroimage 2014 Mar;88:181-7.
    pubmed: 24291503doi: 10.1016/j.neuroimage.2013.11.035google scholar: lookup
  27. Cheng Y, Quinn JF, Weiss LA. An eQTL mapping approach reveals that rare variants in the SEMA5A regulatory network impact autism risk.. Hum Mol Genet 2013 Jul 15;22(14):2960-72.
    pmc: PMC3690972pubmed: 23575222doi: 10.1093/hmg/ddt150google scholar: lookup
  28. Dutton A. Phasing and amplitude of sea-level and climate change during the penultimate interglacial. Nat Geosci 2009;2:355–359.
  29. Durand EY, Patterson N, Reich D, Slatkin M. Testing for ancient admixture between closely related populations.. Mol Biol Evol 2011 Aug;28(8):2239-52.
    pmc: PMC3144383pubmed: 21325092doi: 10.1093/molbev/msr048google scholar: lookup
  30. Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.. PLoS Genet 2012;8(12):e1003125.
    pmc: PMC3527290pubmed: 23284294doi: 10.1371/journal.pgen.1003125google scholar: lookup
  31. Lindsay EH, Opdyke ND, Johnson NM. Pliocene dispersal of the horse Equus and late Cenozoic mammalian dispersal events. Nature 1980;287:135–138.
  32. Steiner CC, Ryder OA. Characterization of Prdm9 in equids and sterility in mules.. PLoS One 2013;8(4):e61746.
    pmc: PMC3632555pubmed: 23613924doi: 10.1371/journal.pone.0061746google scholar: lookup
  33. Cordingley JE. Is the endangered Grevy’s zebra threatened by hybridization?. Anim Conserv 2009;12:505–513.
  34. Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L, Zhai Z, Zhao W, Sun Z, Zhang Y, Meng H, Dugarjaviin M. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.. Sci Rep 2014 May 14;4:4958.
    pmc: PMC4021364pubmed: 24828444doi: 10.1038/srep04958google scholar: lookup
  35. McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.. PLoS One 2014;9(9):e106689.
    pmc: PMC4154752pubmed: 25188499doi: 10.1371/journal.pone.0106689google scholar: lookup
  36. Schubert M, Ermini L, Der Sarkissian C, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.. Nat Protoc 2014 May;9(5):1056-82.
    pubmed: 24722405doi: 10.1038/nprot.2014.063google scholar: lookup
  37. Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.. Bioinformatics 2013 Jul 1;29(13):1682-4.
    pmc: PMC3694634pubmed: 23613487doi: 10.1093/bioinformatics/btt193google scholar: lookup
  38. Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains.. Nature 2014 Jan 2;505(7481):43-9.
    pmc: PMC4031459pubmed: 24352235doi: 10.1038/nature12886google scholar: lookup
  39. Li H, Durbin R. Inference of human population history from individual whole-genome sequences.. Nature 2011 Jul 13;475(7357):493-6.
    pmc: PMC3154645pubmed: 21753753doi: 10.1038/nature10231google scholar: lookup
  40. Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock.. Bioinformatics 2003 Jan 22;19(2):301-2.
    pubmed: 12538260doi: 10.1093/bioinformatics/19.2.301google scholar: lookup
  41. Mayrose I, Barker MS, Otto SP. Probabilistic models of chromosome number evolution and the inference of polyploidy.. Syst Biol 2010 Mar;59(2):132-44.
    pubmed: 20525626doi: 10.1093/sysbio/syp083google scholar: lookup
  42. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood.. Mol Biol Evol 2007 Aug;24(8):1586-91.
    pubmed: 17483113doi: 10.1093/molbev/msm088google scholar: lookup
  43. Sandve GK, Ferkingstad E, Nygård S. Sequential Monte Carlo multiple testing.. Bioinformatics 2011 Dec 1;27(23):3235-41.
    pmc: PMC3223366pubmed: 21998154doi: 10.1093/bioinformatics/btr568google scholar: lookup
  44. Busing F, Meijer E, Van Der Leeden R. Delete-m jackknife for unequal m. Stat Comput 1999;9:2–7.
  45. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data.. PLoS Genet 2012;8(11):e1002967.
    pmc: PMC3499260pubmed: 23166502doi: 10.1371/journal.pgen.1002967google scholar: lookup
  46. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome.. Science 2010 May 7;328(5979):710-722.
    pmc: PMC5100745pubmed: 20448178doi: 10.1126/science.1188021google scholar: lookup
  47. Akaike H. A new look at the statistical model identification. Autom Control IEEE Trans 1974;19:716–723.
  48. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.. PLoS Genet 2009 Oct;5(10):e1000695.
    pmc: PMC2760211pubmed: 19851460doi: 10.1371/journal.pgen.1000695google scholar: lookup
  49. Bates D, Maechler M, Bolker B, Walker S. lme4: Linear mixed-effects models using Eigen and S4. 2014.

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    doi: 10.1371/journal.pone.0286861pubmed: 37289743google scholar: lookup
  2. Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution.. Biology (Basel) 2023 Apr 28;12(5).
    doi: 10.3390/biology12050671pubmed: 37237485google scholar: lookup
  3. Zhang J, Zhao L, Fu Y, Liu F, Wang Z, Li Y, Zhao G, Sun W, Wu B, Song Y, Li S, Hao C, Wuyun B, Wu R, Liu M, Cao G, Nashun B, Surani MA, Sun Q, Bao S, Liu P, Li X. Reprogramming efficiency and pluripotency of mule iPSCs over its parents†.. Biol Reprod 2023 Jun 9;108(6):887-901.
    doi: 10.1093/biolre/ioad041pubmed: 37040346google scholar: lookup
  4. Piras FM, Cappelletti E, Abdelgadir WA, Salamon G, Vignati S, Santagostino M, Sola L, Nergadze SG, Giulotto E. A Satellite-Free Centromere in Equus przewalskii Chromosome 10.. Int J Mol Sci 2023 Feb 18;24(4).
    doi: 10.3390/ijms24044134pubmed: 36835543google scholar: lookup
  5. Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity.. Genes (Basel) 2022 Dec 2;13(12).
    doi: 10.3390/genes13122272pubmed: 36553539google scholar: lookup
  6. Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M. Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule.. Genes (Basel) 2022 Nov 23;13(12).
    doi: 10.3390/genes13122188pubmed: 36553455google scholar: lookup
  7. Wong ELY, Nevado B, Hiscock SJ, Filatov DA. Rapid evolution of hybrid breakdown following recent divergence with gene flow in Senecio species on Mount Etna, Sicily.. Heredity (Edinb) 2023 Jan;130(1):40-52.
    doi: 10.1038/s41437-022-00576-4pubmed: 36494489google scholar: lookup
  8. Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys.. Genes (Basel) 2022 Oct 25;13(11).
    doi: 10.3390/genes13111945pubmed: 36360182google scholar: lookup
  9. Bao W, Yu J, He Y, Liu M, Yang X. The diversity analysis and gene function prediction of intestinal bacteria in three equine species.. Front Microbiol 2022;13:973828.
    doi: 10.3389/fmicb.2022.973828pubmed: 36160217google scholar: lookup
  10. Cirilli O, Machado H, Arroyo-Cabrales J, Barrón-Ortiz CI, Davis E, Jass CN, Jukar AM, Landry Z, Marín-Leyva AH, Pandolfi L, Pushkina D, Rook L, Saarinen J, Scott E, Semprebon G, Strani F, Villavicencio NA, Kaya F, Bernor RL. Evolution of the Family Equidae, Subfamily Equinae, in North, Central and South America, Eurasia and Africa during the Plio-Pleistocene.. Biology (Basel) 2022 Aug 24;11(9).
    doi: 10.3390/biology11091258pubmed: 36138737google scholar: lookup
  11. Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian Fusion and Centromere Repositioning Contributed to the Formation of Satellite-free Centromeres During the Evolution of Zebras.. Mol Biol Evol 2022 Aug 3;39(8).
    doi: 10.1093/molbev/msac162pubmed: 35881460google scholar: lookup
  12. Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene.. Elife 2022 May 11;11.
    doi: 10.7554/eLife.73346pubmed: 35543411google scholar: lookup
  13. Gömer A, Puff C, Reinecke B, Bracht S, Conze M, Baumgärtner W, Steinmann J, Feige K, Cavalleri JMV, Steinmann E, Todt D. Experimental cross-species infection of donkeys with equine hepacivirus and analysis of host immune signatures.. One Health Outlook 2022 May 9;4(1):9.
    doi: 10.1186/s42522-022-00065-ypubmed: 35527255google scholar: lookup
  14. Piras FM, Cappelletti E, Santagostino M, Nergadze SG, Giulotto E, Raimondi E. Molecular Dynamics and Evolution of Centromeres in the Genus Equus.. Int J Mol Sci 2022 Apr 10;23(8).
    doi: 10.3390/ijms23084183pubmed: 35457002google scholar: lookup
  15. Bennett EA, Weber J, Bendhafer W, Champlot S, Peters J, Schwartz GM, Grange T, Geigl EM. The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia.. Sci Adv 2022 Jan 14;8(2):eabm0218.
    doi: 10.1126/sciadv.abm0218pubmed: 35030024google scholar: lookup
  16. Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids.. Commun Biol 2021 Dec 17;4(1):1412.
    doi: 10.1038/s42003-021-02935-zpubmed: 34921240google scholar: lookup
  17. Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation.. Evol Lett 2021 Dec;5(6):568-581.
    doi: 10.1002/evl3.256pubmed: 34917397google scholar: lookup
  18. Päckert M. No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference.. Ecol Evol 2021 Nov;11(22):16354-16364.
    doi: 10.1002/ece3.8199pubmed: 34824832google scholar: lookup
  19. Tombak KJ, Hansen CB, Kinsella JM, Pansu J, Pringle RM, Rubenstein DI. The gastrointestinal nematodes of plains and Grevy's zebras: Phylogenetic relationships and host specificity.. Int J Parasitol Parasites Wildl 2021 Dec;16:228-235.
    doi: 10.1016/j.ijppaw.2021.10.007pubmed: 34712556google scholar: lookup
  20. Mallet J. Alternative views of biological species: reproductively isolated units or genotypic clusters?. Natl Sci Rev 2020 Aug;7(8):1401-1407.
    doi: 10.1093/nsr/nwaa116pubmed: 34692169google scholar: lookup
  21. Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-Del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes.. Nature 2021 Oct;598(7882):634-640.
    doi: 10.1038/s41586-021-04018-9pubmed: 34671162google scholar: lookup
  22. Li S, Zhao G, Han H, Li Y, Li J, Wang J, Cao G, Li X. Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study.. BMC Genomics 2021 Sep 15;22(1):665.
    doi: 10.1186/s12864-021-07984-6pubmed: 34521340google scholar: lookup
  23. Wang Y, Miao X, Zhao Z, Wang Y, Li S, Wang C. Transcriptome Atlas of 16 Donkey Tissues.. Front Genet 2021;12:682734.
    doi: 10.3389/fgene.2021.682734pubmed: 34434218google scholar: lookup
  24. Zeng L, Liu HQ, Tu XL, Ji CM, Gou X, Esmailizadeh A, Wang S, Wang MS, Wang MC, Li XL, Charati H, Adeola AC, Moshood Adedokun RA, Oladipo O, Olaogun SC, Sanke OJ, Godwin F M, Cecily Ommeh S, Agwanda B, Kasiiti Lichoti J, Han JL, Zheng HK, Wang CF, Zhang YP, Frantz LAF, Wu DD. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation.. Zool Res 2021 Jul 18;42(4):450-460.
    doi: 10.24272/j.issn.2095-8137.2021.095pubmed: 34156172google scholar: lookup
  25. Cirilli O, Pandolfi L, Rook L, Bernor RL. Evolution of Old World Equus and origin of the zebra-ass clade.. Sci Rep 2021 May 12;11(1):10156.
    doi: 10.1038/s41598-021-89440-9pubmed: 33980921google scholar: lookup
  26. Edwards JE, Shetty SA, van den Berg P, Burden F, van Doorn DA, Pellikaan WF, Dijkstra J, Smidt H. Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species.. Anim Microbiome 2020 Feb 12;2(1):6.
    doi: 10.1186/s42523-020-0023-1pubmed: 33499982google scholar: lookup
  27. Edwards JE, Schennink A, Burden F, Long S, van Doorn DA, Pellikaan WF, Dijkstra J, Saccenti E, Smidt H. Domesticated equine species and their derived hybrids differ in their fecal microbiota.. Anim Microbiome 2020 Mar 16;2(1):8.
    doi: 10.1186/s42523-020-00027-7pubmed: 33499942google scholar: lookup
  28. Câmara RJF, Bueno BL, Resende CF, Balasuriya UBR, Sakamoto SM, Reis JKPD. Viral Diseases that Affect Donkeys and Mules.. Animals (Basel) 2020 Nov 25;10(12).
    doi: 10.3390/ani10122203pubmed: 33255568google scholar: lookup
  29. Garcia-Erill G, Kjaer MM, Albrechtsen A, Siegismund HR, Heller R. Vicariance followed by secondary gene flow in a young gazelle species complex.. Mol Ecol 2021 Jan;30(2):528-544.
    doi: 10.1111/mec.15738pubmed: 33226701google scholar: lookup
  30. Özkan Ünal E, Özdil F, Kaplan S, Gürcan EK, Genç S, Arat S, Soysal Mİ. Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region.. Animals (Basel) 2020 Oct 27;10(11).
    doi: 10.3390/ani10111970pubmed: 33120938google scholar: lookup
  31. Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae.. BMC Genomics 2020 Sep 30;21(1):677.
    doi: 10.1186/s12864-020-07089-6pubmed: 32998693google scholar: lookup
  32. Novikova PY, Brennan IG, Booker W, Mahony M, Doughty P, Lemmon AR, Moriarty Lemmon E, Roberts JD, Yant L, Van de Peer Y, Keogh JS, Donnellan SC. Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus.. PLoS Genet 2020 May;16(5):e1008769.
    doi: 10.1371/journal.pgen.1008769pubmed: 32392206google scholar: lookup
  33. Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective.. Int J Mol Sci 2020 Apr 18;21(8).
    doi: 10.3390/ijms21082838pubmed: 32325780google scholar: lookup
  34. Hamlin JAP, Hibbins MS, Moyle LC. Assessing biological factors affecting postspeciation introgression.. Evol Lett 2020 Apr;4(2):137-154.
    doi: 10.1002/evl3.159pubmed: 32313689google scholar: lookup
  35. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.. Anim Genet 2019 Dec;50(6):569-597.
    doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
  36. Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.. Cell 2019 May 30;177(6):1419-1435.e31.
    doi: 10.1016/j.cell.2019.03.049pubmed: 31056281google scholar: lookup
  37. Savriama Y, Valtonen M, Kammonen JI, Rastas P, Smolander OP, Lyyski A, Häkkinen TJ, Corfe IJ, Gerber S, Salazar-Ciudad I, Paulin L, Holm L, Löytynoja A, Auvinen P, Jernvall J. Bracketing phenogenotypic limits of mammalian hybridization.. R Soc Open Sci 2018 Nov;5(11):180903.
    doi: 10.1098/rsos.180903pubmed: 30564397google scholar: lookup
  38. Novak BJ. De-Extinction.. Genes (Basel) 2018 Nov 13;9(11).
    doi: 10.3390/genes9110548pubmed: 30428542google scholar: lookup
  39. MacGuigan DJ, Near TJ. Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae).. Syst Biol 2019 Mar 1;68(2):329-346.
    doi: 10.1093/sysbio/syy074pubmed: 30395332google scholar: lookup
  40. Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, Montero MM, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. Interspecific Gene Flow Shaped the Evolution of the Genus Canis.. Curr Biol 2018 Nov 5;28(21):3441-3449.e5.
    doi: 10.1016/j.cub.2018.08.041pubmed: 30344120google scholar: lookup
  41. Beeravolu CR, Hickerson MJ, Frantz LAF, Lohse K. ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.. Genome Biol 2018 Sep 25;19(1):145.
    doi: 10.1186/s13059-018-1517-ypubmed: 30253810google scholar: lookup
  42. Zhu H, Gifford RJ, Murcia PR. Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes.. J Virol 2018 Dec 1;92(23).
    doi: 10.1128/JVI.00927-18pubmed: 30209175google scholar: lookup
  43. Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA, Love CC, Varner DD, Bellott DW, Murphy WJ, Chowdhary BP, Raudsepp T. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.. Nat Commun 2018 Jul 27;9(1):2945.
    doi: 10.1038/s41467-018-05290-6pubmed: 30054462google scholar: lookup
  44. Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. Improved de novo genomic assembly for the domestic donkey.. Sci Adv 2018 Apr;4(4):eaaq0392.
    doi: 10.1126/sciadv.aaq0392pubmed: 29740610google scholar: lookup
  45. Pazza R, Dergam JA, Kavalco KF. Trends in Karyotype Evolution in Astyanax (Teleostei, Characiformes, Characidae): Insights From Molecular Data.. Front Genet 2018;9:131.
    doi: 10.3389/fgene.2018.00131pubmed: 29713335google scholar: lookup
  46. Zheng Y, Janke A. Gene flow analysis method, the D-statistic, is robust in a wide parameter space.. BMC Bioinformatics 2018 Jan 8;19(1):10.
    doi: 10.1186/s12859-017-2002-4pubmed: 29310567google scholar: lookup
  47. Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A. Speciation Generates Mosaic Genomes in Kangaroos.. Genome Biol Evol 2018 Jan 1;10(1):33-44.
    doi: 10.1093/gbe/evx245pubmed: 29182740google scholar: lookup
  48. Heintzman PD, Zazula GD, MacPhee R, Scott E, Cahill JA, McHorse BK, Kapp JD, Stiller M, Wooller MJ, Orlando L, Southon J, Froese DG, Shapiro B. A new genus of horse from Pleistocene North America.. Elife 2017 Nov 28;6.
    doi: 10.7554/eLife.29944pubmed: 29182148google scholar: lookup
  49. Anderson DG, Kvie KS, Davydov VN, Røed KH. Maintaining genetic integrity of coexisting wild and domestic populations: Genetic differentiation between wild and domestic Rangifer with long traditions of intentional interbreeding.. Ecol Evol 2017 Sep;7(17):6790-6802.
    doi: 10.1002/ece3.3230pubmed: 28904760google scholar: lookup
  50. Vecchione C, Villa F, Carrizzo A, Spinelli CC, Damato A, Ambrosio M, Ferrario A, Madonna M, Uccellatore A, Lupini S, Maciag A, Ryskalin L, Milanesi L, Frati G, Sciarretta S, Bellazzi R, Genovese S, Ceriello A, Auricchio A, Malovini A, Puca AA. A rare genetic variant of BPIFB4 predisposes to high blood pressure via impairment of nitric oxide signaling.. Sci Rep 2017 Aug 29;7(1):9706.
    doi: 10.1038/s41598-017-10341-xpubmed: 28852218google scholar: lookup
  51. Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds.. BMC Genomics 2017 Jul 27;18(1):565.
    doi: 10.1186/s12864-017-3943-8pubmed: 28750625google scholar: lookup
  52. Kang L, Garner HR, Price DK, Michalak P. A Test for Gene Flow among Sympatric and Allopatric Hawaiian Picture-Winged Drosophila.. J Mol Evol 2017 Jun;84(5-6):259-266.
    doi: 10.1007/s00239-017-9795-7pubmed: 28492967google scholar: lookup
  53. Cucchi T, Mohaseb A, Peigné S, Debue K, Orlando L, Mashkour M. Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies.. R Soc Open Sci 2017 Apr;4(4):160997.
    doi: 10.1098/rsos.160997pubmed: 28484618google scholar: lookup
  54. Bennett EA, Champlot S, Peters J, Arbuckle BS, Guimaraes S, Pruvost M, Bar-David S, Davis SJM, Gautier M, Kaczensky P, Kuehn R, Mashkour M, Morales-Muñiz A, Pucher E, Tournepiche JF, Uerpmann HP, Bălăşescu A, Germonpré M, Gündem CY, Hemami MR, Moullé PE, Ötzan A, Uerpmann M, Walzer C, Grange T, Geigl EM. Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA.. PLoS One 2017;12(4):e0174216.
    doi: 10.1371/journal.pone.0174216pubmed: 28422966google scholar: lookup
  55. Kumar V, Lammers F, Bidon T, Pfenninger M, Kolter L, Nilsson MA, Janke A. The evolutionary history of bears is characterized by gene flow across species.. Sci Rep 2017 Apr 19;7:46487.
    doi: 10.1038/srep46487pubmed: 28422140google scholar: lookup
  56. Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA.. Syst Biol 2017 Jan 1;66(1):e1-e29.
    doi: 10.1093/sysbio/syw059pubmed: 28173586google scholar: lookup
  57. Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes.. Philos Trans R Soc Lond B Biol Sci 2017 Feb 5;372(1713).
    doi: 10.1098/rstb.2015.0484pubmed: 27994125google scholar: lookup
  58. Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M, Orlando L. The Evolutionary Origin and Genetic Makeup of Domestic Horses.. Genetics 2016 Oct;204(2):423-434.
    doi: 10.1534/genetics.116.194860pubmed: 27729493google scholar: lookup
  59. Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.. Mol Biol Evol 2016 Dec;33(12):3284-3298.
    doi: 10.1093/molbev/msw184pubmed: 27624717google scholar: lookup
  60. Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krämer U, Koch MA, Nordborg M. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.. Nat Genet 2016 Sep;48(9):1077-82.
    doi: 10.1038/ng.3617pubmed: 27428747google scholar: lookup
  61. Solís-Lemus C, Ané C. Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.. PLoS Genet 2016 Mar;12(3):e1005896.
    doi: 10.1371/journal.pgen.1005896pubmed: 26950302google scholar: lookup
  62. Rosenzweig BK, Pease JB, Besansky NJ, Hahn MW. Powerful methods for detecting introgressed regions from population genomic data.. Mol Ecol 2016 Jun;25(11):2387-97.
    doi: 10.1111/mec.13610pubmed: 26945783google scholar: lookup
  63. Pease JB, Haak DC, Hahn MW, Moyle LC. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.. PLoS Biol 2016 Feb;14(2):e1002379.
    doi: 10.1371/journal.pbio.1002379pubmed: 26871574google scholar: lookup
  64. Bayerova Z, Janova E, Matiasovic J, Orlando L, Horin P. Positive selection in the SLC11A1 gene in the family Equidae.. Immunogenetics 2016 May;68(5):353-64.
    doi: 10.1007/s00251-016-0905-2pubmed: 26846480google scholar: lookup
  65. Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation.. Mol Ecol 2016 Jun;25(11):2337-60.
    doi: 10.1111/mec.13557pubmed: 26836441google scholar: lookup
  66. Mallet J, Besansky N, Hahn MW. How reticulated are species?. Bioessays 2016 Feb;38(2):140-9.
    doi: 10.1002/bies.201500149pubmed: 26709836google scholar: lookup
  67. Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.. Proc Natl Acad Sci U S A 2015 Dec 15;112(50):E6889-97.
    doi: 10.1073/pnas.1513696112pubmed: 26598656google scholar: lookup
  68. Sun Y, Jiang Q, Yang C, Wang X, Tian F, Wang Y, Ma Y, Ju Z, Huang J, Zhou X, Zhong J, Wang C. Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis.. Curr Genet 2016 May;62(2):383-90.
    doi: 10.1007/s00294-015-0531-9pubmed: 26527116google scholar: lookup
  69. Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.. Genome Biol 2015 Oct 26;16:234.
    doi: 10.1186/s13059-015-0790-2pubmed: 26498365google scholar: lookup
  70. Brinkmann J, Koudelka T, Keppler JK, Tholey A, Schwarz K, Thaller G, Tetens J. Characterization of an Equine α-S2-Casein Variant Due to a 1.3 kb Deletion Spanning Two Coding Exons.. PLoS One 2015;10(10):e0139700.
    doi: 10.1371/journal.pone.0139700pubmed: 26444874google scholar: lookup
  71. Orlando L, Gilbert MT, Willerslev E. Reconstructing ancient genomes and epigenomes.. Nat Rev Genet 2015 Jul;16(7):395-408.
    doi: 10.1038/nrg3935pubmed: 26055157google scholar: lookup
  72. Der Sarkissian C, Vilstrup JT, Schubert M, Seguin-Orlando A, Eme D, Weinstock J, Alberdi MT, Martin F, Lopez PM, Prado JL, Prieto A, Douady CJ, Stafford TW, Willerslev E, Orlando L. Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids.. Biol Lett 2015 Mar;11(3).
    doi: 10.1098/rsbl.2014.1058pubmed: 25762573google scholar: lookup
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